[1] The absence of dams on the river causes its flow to greatly fluctuate throughout the year depending on snowpack and rainfall within the watershed.

[3][10] The main branch of the John Day River rises in the Strawberry Mountains in eastern Grant County.

At Dayville, in western Grant County, it is joined from the south by the South Fork John Day River, then flows north through Picture Gorge and the Sheep Rock Unit of the John Day Fossil Beds National Monument.

The John Day River joins the Columbia from the southeast approximately 16 miles (26 km) northeast of Biggs.

The John Day is navigable by rafts and other small river craft by boaters who obtain permits provided by the Bureau of Land Management.

[4] In 1988, the United States Congress designated 147.5 miles (237.4 km) of the river from Service Creek to Tumwater Falls as Wild and Scenic for its recreational opportunities.

The segment of the river is a popular destination for anadromous steelhead and warm water bass fishing, as well as whitewater rafting.